Efficient multiple time scale molecular dynamics: using colored noise thermostats to stabilize resonances

TL;DR

This paper introduces a colored noise thermostatting scheme for multiple time scale molecular dynamics that targets high frequency modes, enabling larger time steps without sacrificing accuracy or perturbing dynamics.

Contribution

The authors propose a simple colored noise thermostat that alleviates resonance issues in multiple time scale MD, allowing larger time steps as an alternative to constraints.

Findings

Enables larger outer time steps in MD simulations.

Maintains accurate sampling and minimal dynamic perturbation.

Comparable to constraining fast motions.

Abstract

Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice the largest outer time step possible is limited not by the physical forces but by resonances between the fast and slow modes. In this paper we show that this problem can be alleviated by using a simple colored noise thermostatting scheme which selectively targets the high frequency modes in the system. For two sample problems, flexible water and solvated alanine dipeptide, we demonstrate that this allows the use of large outer time steps while still obtaining accurate sampling and minimizing the perturbation of the dynamics. Furthermore, this approach is shown to be comparable to constraining fast motions, thus providing an alternative to molecular dynamics with constraints.